Oropharyngeal candidiasis is often the earliest detectable clinical manifestation of infection with Human Immunodeficiency Virus (HIV) and the most prevalent opportunistic infection observed in patients with Acquired Immunodeficiency Syndrome (AIDS). C. albicans and other Candida species are the most frequent causes of oropharyngeal candidiasis and esophageal candidiasis. Resistance to antifungal drugs is of particular concern given the limited number of clinically useful antifungals. This concern is especially critical for the growing population of immunocompromised individuals, especially in the third world, who receive extended courses of prophylactic antifungal therapy. In the previous funding cycle we made the major discovery that aneuploidy is acquired at high frequency when cells are exposed to azole antifungals and that a specific aneuploidy, isochromosome 5L, causes azole resistance by increasing the copy number of genes on the left arm of Chromosome 5. Since then, aneuploidy has been found in other human fungal pathogens. Important new data presented here indicates that aneuploidy is prevalent in strains resistant to the newest class of antifungals, the echinocandins. This competing renewal application proposes to continue our work on genome integrity in C. albicans, with a particular emphasis on how the genome responds to antifungal drug stress: how it increases levels of recombination and undergoes changes in chromosome copy number. Our long-term goal is to understand the mechanisms that pathogenic fungi use to evolve, especially in response to antifungals, so that new therapeutic approaches that interfere with those mechanisms can be developed. The processes that enable cells to survive in the presence of antifungals are potential targets of companion therapies that would extend the life span of the limited arsenal of available antifungals. Once we have develop the appropriate tools, we will ask if non-albicans Candida species, which are naturally more resistant to antifungal drugs, use a similar repertoire of mechanisms of antifungal drug resistance. We will test several working hypotheses raised by our previous work: a) Aneuploidy and/or LOH are common mechanisms used by pathogenic fungi to cope with assault from distinct classes of antifungal agents that use different mechanisms of action; b) Specific sub- populations of cells acquire high levels of aneuploidy and/or are hyper-recombinogenic; and c) Tetraploid intermediates form in response to drug stress and then undergo concerted chromosome loss and/or concerted recombination events to generate diverse progeny, some of which are better able to survive under stress conditions. We have developed a powerful set of tools to analyze the rates and types of genome changes that arise in C. albicans. Here we will use them to identify 1) the types of genome changes associated with echinocandin resistance, 2) the mechanisms that result in hyper-recombination and aneuploidy that occur in response to antifungals and 3) the role of tetraploidy in the response to antifungal drugs.